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Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure

Reuben Thomas1†, Julia M Gohlke1†, Geffrey F Stopper2, Frederick M Parham1 and Christopher J Portier1*

1 Environmental Systems Biology Group, Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, RTP, NC 27709, USA

2 Department of Biology, Sacred Heart University, Fairfield, CT 06825, USA

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Genome Biology 2009, 10:R44 doi:10.1186/gb-2009-10-4-r44

Published: 24 April 2009

Additional files

Additional data file 1:

Estimation of P-values and additional tables of results.

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Additional data file 2:

The nodes of this network are pathways while the edges indicate the transfer of signal or material between the pathways.

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Additional data file 3:

(a) Sensitivity versus '1 - specificity' of enriched pathways that are predictive of survival from lung cancer for the six methods: SEPEA_NT1, SEPEA_NT1*, SEPEA_NT2, SEPEA_NT3, GSEA and maxmean. SEPEA_NT1* is the same analysis as in SEPEA_NT1 except that the pathway network information was not used. (b) Positive predictive power (ppp) versus negative predictive power (npp) for the same data and using the same methods of analysis as in (a).

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Additional data file 4:

P-values for KEGG [44] pathways after cyclopamine treatment of developing X. laevis, designed to inhibit SHH signaling, using microarray data from GEO [45] [GEO:GSE8293]. P-values were obtained using SEPEA_NT1, SEPEA_NT2, SEPEA_NT3, GSEA and maxmean analyses with 1,000 randomizations to compute significance.

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